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<ol class="content-list">

<li><a href="#cpi">CPMD Input File</a></li>

<li><a href="#cube">Gaussian Cube file</a></li>

<li><a href="#dmp">Lammps Dump</a></li>

<li><a href="#json">json</a></li>

<li><a href="#lmp">Lammps Data File</a></li>

<li><a href="#orca">ORCA Input File</a></li>

<li><a href="#pos">VASP POSCAR</a></li>

<li><a href="#pwi">PWScf Input File</a></li>

<li><a href="#pwo">PWScf Output File</a></li>

<li><a href="#xsf">XCrysDen Structure File</a></li>

<li><a href="#xyz">xyz</a></li>

</ol>

<div class="content-text">
<p>
Vipster supports various different formats describing atomic structures.
It is written with no specific format in mind.
</p>
<p>
Whenever a format provides or requires additional data that is not tied to the atomic structure,
this is encapsulated in a Parameter set.
For example, the control blocks configuring a quantum chemical simulation can be read from a file,
saved and then later be reused for setting up a series of other calculations with other molecules,
but the same calculation settings.
</p>
<p>
If a file format supports multiple ways to print the atomic structure,
this can be controlled with an (output) preset.
These can e.g. be used to select between printing the structure in Ångström with charges
or in Bohr units with the list of bonds.
</p>
<p>
The following plugins are included in a default installation:
</p>
</div>


<div class="content-text highlight">
    <a class="anchor" id="cpi"></a>
    <h1>
        CPMD Input File
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--cpi</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.cpi</code></div>
    
        
        <div class="highlight highlight-nested">
        <h2>Parameters</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>&amp;ATOMS: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.
Vipster automatically fills in supported information:
Atomic positions, ISOTOPE and pseudo-potential information and &#39;FIX ATOMS&#39; or &#39;FIX COORDINATES&#39; constraints.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;CLASSIC: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;CPMD: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;DFT: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;EXTE: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;HARDNESS: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;INFO: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;LINRES: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;PATH: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;PIMD: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;PROP: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;PTDDFT: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;QMMM: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;RESP: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;SYSTEM: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.
Vipster automatically fills in supported information:
CELL VECTORS, KPOINTS and ANGSTROM/SCALE keywords according to I/O preset.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;TDDFT: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;VDW: [str]</code></p>
            <p>Raw-text section that will be written to input file. See CPMD documentation for valid contents.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>PPNonlocality: str</code></p>
            <p>The default non-locality for pseudo-potentials.
Will be printed as-is if the periodic table entry for the current type does not contain an explicit non-locality string.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>PPPrefix: str</code></p>
            <p>The default prefix for pseudo-potentials.
Will be prepended to the type name if the periodic table entry for this type does not contain an explicit pseudo-potential name.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>PPSuffix: str</code></p>
            <p>The default suffix for pseudo-potentials.
Will be appended to the type name if the periodic table entry for this type does not contain an explicit pseudo-potential name.</p>
            </li>
        
        </ul>
        </div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>fmt: {&#39;Crystal&#39;, &#39;Alat&#39;, &#39;Angstrom&#39;, &#39;Bohr&#39;, &#39;Active&#39;}</code></p>
            <p>Active: Use the current Step&#39;s active atom format
Else: Enforce the selected atom format</p>
            </li>
        
        </ul>
        </div>
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="cube"></a>
    <h1>
        Gaussian Cube file
        
        (read only)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--cube</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.cube</code></div>
    
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="dmp"></a>
    <h1>
        Lammps Dump
        
        (read only)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--dmp</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.lammpstrj</code></div>
    
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="json"></a>
    <h1>
        json
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--json</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.json</code></div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>bonds: bool</code></p>
            <p>Export bonds</p>
            </li>
        
            
            <li class="highlight">
            <p><code>cell: bool</code></p>
            <p>Write with cell</p>
            </li>
        
            
            <li class="highlight">
            <p><code>elements: {&#39;none&#39;, &#39;custom&#39;, &#39;used&#39;, &#39;all&#39;}</code></p>
            <p>Store atom types
Custom: save only types not in the global table
Used: save all types that are used by any atom
All: save all types in the molecules&#39; own table</p>
            </li>
        
            
            <li class="highlight">
            <p><code>fmt: {&#39;active&#39;, &#39;crystal&#39;, &#39;alat&#39;, &#39;angstrom&#39;, &#39;bohr&#39;}</code></p>
            <p>Active: use the current Step&#39;s active atom format
Else: enforce the selected format</p>
            </li>
        
            
            <li class="highlight">
            <p><code>indent: bool</code></p>
            <p>Pretty-print output so not everything is on one line</p>
            </li>
        
            
            <li class="highlight">
            <p><code>trajectory: bool</code></p>
            <p>Write complete trajectory instead of single step</p>
            </li>
        
        </ul>
        </div>
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="lmp"></a>
    <h1>
        Lammps Data File
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--lmp</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.lmp</code></div>
    
        
        <div class="highlight highlight-nested">
        <h2>Parameters</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>Angle Coeff: {str: str}</code></p>
            <p>If the IOPreset enables both angle and parameter printing, parameters will be looked up according to the angle type. Missing types will use the fallback (if present) or cause an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Angle Coeff Fallback: str</code></p>
            <p>If this value is present, it will be used if a angle type can not be found in the Angle Coeff map. If it is absent, missing angle types are an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Bond Coeff: {str: str}</code></p>
            <p>If the IOPreset enables both bond and parameter printing, parameters will be looked up according to the bond type. Missing types will use the fallback (if present) or cause an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Bond Coeff Fallback: str</code></p>
            <p>If this value is present, it will be used if a bond type can not be found in the Bond Coeff map. If it is absent, missing bond types are an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Dihedral Coeff: {str: str}</code></p>
            <p>If the IOPreset enables both dihedral and parameter printing, parameters will be looked up according to the dihedral type. Missing types will use the fallback (if present) or cause an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Dihedral Coeff Fallback: str</code></p>
            <p>If this value is present, it will be used if a dihedral type can not be found in the Dihedral Coeff map. If it is absent, missing dihedral types are an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Improper Coeff: {str: str}</code></p>
            <p>If the IOPreset enables both improper and parameter printing, parameters will be looked up according to the improper type. Missing types will use the fallback (if present) or cause an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Improper Coeff Fallback: str</code></p>
            <p>If this value is present, it will be used if a improper type can not be found in the Improper Coeff map. If it is absent, missing improper types are an error.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>Pair Coeff: {str: str}</code></p>
            <p>If the IOPreset enables parameter printing, pair coefficients are looked up according the atom type. Missing types will cause an error.</p>
            </li>
        
        </ul>
        </div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>angles: bool</code></p>
            <p>Toggle printing angles (extrapolated from bond network)</p>
            </li>
        
            
            <li class="highlight">
            <p><code>bonds: bool</code></p>
            <p>Toggle printing bonds (taken directly from Step)</p>
            </li>
        
            
            <li class="highlight">
            <p><code>coeff: bool</code></p>
            <p>Toggle printing parameters from parameter set</p>
            </li>
        
            
            <li class="highlight">
            <p><code>dihedrals: bool</code></p>
            <p>Toggle printing dihedrals (extrapolated from bond network)</p>
            </li>
        
            
            <li class="highlight">
            <p><code>impropers: bool</code></p>
            <p>Toggle printing impropers (extrapolated from bond network)</p>
            </li>
        
            
            <li class="highlight">
            <p><code>style: {&#39;angle&#39;, &#39;atomic&#39;, &#39;bond&#39;, &#39;charge&#39;, &#39;full&#39;, &#39;molecular&#39;}</code></p>
            <p>The atom_style to be used by Lammps.
See https://lammps.sandia.gov/doc/atom_style.html for details.</p>
            </li>
        
        </ul>
        </div>
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="orca"></a>
    <h1>
        ORCA Input File
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--orca</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.inp</code></div>
    
        
        <div class="highlight highlight-nested">
        <h2>Parameters</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>header: [str]</code></p>
            <p>Raw text header to be printed above coordinates.
See ORCA documentation for details.</p>
            </li>
        
        </ul>
        </div>
    
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="pos"></a>
    <h1>
        VASP POSCAR
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--pos</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>POSCAR</code></div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>cartesian: bool</code></p>
            <p>Toggle between cartesian (Å) and direct (crystal) coordinates.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>selective: bool</code></p>
            <p>Toggles selective dynamics.

If &#39;true&#39;, atom-coordinates can be kept fixed during simulation.</p>
            </li>
        
        </ul>
        </div>
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="pwi"></a>
    <h1>
        PWScf Input File
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--pwi</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.pwi</code></div>
    
        
        <div class="highlight highlight-nested">
        <h2>Parameters</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>&amp;CELL: {str: str}</code></p>
            <p>&amp;CELL namelist controls how the cell will react to pressure.
Only needed in variable-cell calculations.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;CONTROL: {str: str}</code></p>
            <p>&amp;CONTROL namelist specifies the type of calculation and general runtime settings.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;ELECTRONS: {str: str}</code></p>
            <p>&amp;ELECTRONS namelist controls how the SCF calculations are performed.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;IONS: {str: str}</code></p>
            <p>&amp;IONS namelist controls how atoms are propagated.
Only needed in relax and MD calculations.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>&amp;SYSTEM: {str: str}</code></p>
            <p>&amp;SYSTEM namelist contains details about the unit-cell.
Necessary details will be provided by Vipster (ibrav, nat, ntyp, celldm/A).</p>
            </li>
        
            
            <li class="highlight">
            <p><code>PPPrefix: str</code></p>
            <p>The default prefix for pseudo-potentials.
Will be prepended to the type name if the periodic table entry for this type does not contain an explicit pseudo-potential name.</p>
            </li>
        
            
            <li class="highlight">
            <p><code>PPSuffix: str</code></p>
            <p>The default suffix for pseudo-potentials.
Will be appended to the type name if the periodic table entry for this type does not contain an explicit pseudo-potential name.</p>
            </li>
        
        </ul>
        </div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>atoms: {&#39;Crystal&#39;, &#39;Alat&#39;, &#39;Angstrom&#39;, &#39;Bohr&#39;, &#39;Active&#39;}</code></p>
            <p>Active: Use the current Step&#39;s active atom format
Else: Enforce the selected format</p>
            </li>
        
            
            <li class="highlight">
            <p><code>cell: {&#39;Angstrom&#39;, &#39;Bohr&#39;, &#39;Active&#39;}</code></p>
            <p>Active: Match current Step&#39;s active atom format (Å if Å, Bohr otherwise)
Else: Enforce the selected format</p>
            </li>
        
        </ul>
        </div>
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="pwo"></a>
    <h1>
        PWScf Output File
        
        (read only)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--pwo</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.pwo</code></div>
    
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="xsf"></a>
    <h1>
        XCrysDen Structure File
        
        (read only)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--xsf</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.xsf</code></div>
    
    
</div>

<div class="content-text highlight">
    <a class="anchor" id="xyz"></a>
    <h1>
        xyz
        
        (read/write)
        
    </h1>
    <div class="highlight highlight-nested">Command line argument: <code>--xyz</code></div>
    <div class="highlight highlight-nested">Matches files named: <code>*.xyz</code></div>
    
    
        
        <div class="highlight highlight-nested">
        <h2>Output preset</h2>
        <ul class="code">
        
            
            <li class="highlight">
            <p><code>atomdata: {&#39;None&#39;, &#39;Charge&#39;, &#39;Forces&#39;}</code></p>
            <p>None: Write only coordinates (standard xyz)
Charge: Append a column containing the atomic charges
Forces: Append three columns containing the atomic forces</p>
            </li>
        
            
            <li class="highlight">
            <p><code>filemode: {&#39;Step&#39;, &#39;Trajec&#39;, &#39;Cell&#39;}</code></p>
            <p>Step: Write currently active Step
Trajec: Write complete trajectory of active Molecule
Cell: Write currently active Step and append the unit cell</p>
            </li>
        
        </ul>
        </div>
    
</div>

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